[gmx-users] pca on amber MD output

[nadiav at soton.ac.uk]

Thank you all for your replies. It has been very helpful.

Kind regards

Nadia


Quoting Tsjerk Wassenaar <tsjerkw at gmail.com>:

> Hi Nadia,
>
> Gromacs reads .pdb files (single or multimodel ones) perfectly. The
> programmers have noted that .pdb files are in Angstroms usually.
> Besides, you don't need an additional .pdb file when reading a .pdb
> trajectory (if required you can give the same file as a structure
> file).
>
> Cheers,
>
> Tsjerk
>
> On 10/6/06, nadiav at soton.ac.uk <nadiav at soton.ac.uk> wrote:
> >
> > Hi Mark,
> >
> > Thank you very much for the clarification.  I am also testing this at
> the
> > moment running with and without Anstroms/nm conversions.
> >
> > Regards,
> >
> > Nadia
> >
> >
> > Quoting Mark Abraham <Mark.Abraham at anu.edu.au>:
> >
> > > nadiav at soton.ac.uk wrote:
> > > > Hi gromacs users,
> > > >
> > > > I am a new user to gromacs and realise that there are lots of
> comments
> > > on
> > > > the archive already about using gromacs with amber outputs but I am
> > > getting
> > > > rather mixed messages.
> > > >
> > > > I would like to clarify a few things.  I have an Amber trjectory
> file
> > > saved
> > > > through VMD in a .pdb format and a pdb file for the topology.
> > > >
> > > > I see that some say that one should convert the trajectory file,
> some
> > > say
> > > > that gromacs reads .pdb and others mention changing the extension
> to
> > > .g87
> > > > and so on.  My main question is about the fact that amber works in
> > > > Angstroms and gromacs in nm.  Should I convert my trajectory.pdb
> and
> > > > topology.pdb to nm before carrying out principal component
> analysis?
> > >
> > > There would be no need, since PCA is scale-independent. Further, the
> PDB
> > > format prescribes the use of Angstroms, so I expect any software to
> > > presume the use of Angstroms in any PDB file (since they can't tell
> the
> > > point of origin of the PDB file). You could, of course, test this
> > > yourself.
> > >
> > > Mark
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> >
> >
> >
> >
> >
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> Dept. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4
> 9747AG Groningen, The Netherlands
> +31 50 363 4336
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